He is the Mexican American FBI Agent assigned to guard Sami Brady after she goes into witness protection following the murder of mayor Anthony Marino. Rafe falls in love with Sami while they are together, even after Sami learns she is pregnant with EJ's child. Nicole DiMera switched Sami's baby (Sydney) after she was born. Rafe agrees to stay in Salem to be near Sami and, together, they fabricate a story to make everyone believe Grace was adopted from an orphanage. Rafe initiates adoption proceedings to become Grace's legal father, but the baby suddenly dies from bacterial meningitis. He finds that Nicole DiMera miscarried her baby and switched Grace with Sydney, Sami's biological daughter. While trying to collect clues to support this theory, his deceased fiancee Emily Hudson's sister, Meredith, kidnapps him and holds him hostage. Meredith built a brick wall to hold him in so that he can't escape and dumps him into the harbor where Dr. Carly Manning saves his life. Rafe comes back trying to prove that Sami's baby is Sydney. He proves it by having a DNA test done on Sydney's teething ring and Sami's toothbrush. Stefano tries to kill him, but EJ saves his life.
Rafe Hernandez first comes on screen on October 31st 2008, as the FBI agent assigned for Sami Brady. Little does Rafe know that Sami is pregnant with none other than EJ Dimera's child, despite this Rafe agrees to help Sami out. Rafe begins investigating and eventually finds out that Nicole Dimera switched the babies because she miscarried her child with EJ. Sami and Sydney are reunited as are Sami and Rafe. On September 26 Sami finds out from Rafe that EJ was the one that kidnapped their daughter Sydney. Rafe and Sami rekindle their romance. Days later Sami shoots EJ in the head. When Rafe finds out he agrees to keep it a secret. Rafe's sister Arianna Hernandez died in a tragic hit and run accident. In December of 2010 Rafe and Sami are married in a beautiful ceremony in the park. But their marriage is short lived when EJ interrupts the wedding and takes Johnny and Sydney away from Sami. In 2011 Rafe gets kidnapped by the dastardly EJ and Stefano Dimera only to be replaced by a doppelganger. Rafe is in a holding cell for months until he loses his memory. In may 2011 Sami and Rafe are reunited and they rekindle their love. Sami and Rafe are doing great together till Johnny goes missing, and Sami has angry grief sex with EJ.
Rafe and Sami are happy together until he overhears Will telling Sonny that Sami slept with EJ. Angry, Rafe confronts Sami about her actions, who does not deny that she slept with EJ. EJ is about to propose to Nicole when Rafe interrupts and tells Nicole the truth: that EJ slept with Sami. Nicole devastated at hearing this decides to throw the ring in EJ's face. Days later Rafe finds out that Nicole is pregnant with EJ's baby. Rafe agrees to keep the baby a secret and tells EJ that he is the father of the baby. However EJ does not believe that Rafe is the father so he decides to take a DNA test. EJ eventually learns that Rafe is indeed the father of Nicole's baby. But EJ continues to harass Nicole and Rafe keeps stepping in to defend her. Throughout her pregnancy Nicole and Rafe have formed a special bond. On October 15 2012 Rafe finds out that Nicole lost her baby and he decides to grieve along with his best friend. On October 16 2012 Sami finds out that Rafe lied to her about the paternity and feels betrayed, but they eventually manage to say friends.
Rafe starts a sexual relationship with the newly single Kate Roberts. He is also weary of Gabi's relationship with ex-convict Nick Fallon. Rafe learns Gabi is pregnant with Nick's child, but in 2014, it is discovered, at Nick and Gabi's wedding, that Will is actually the father. Sami lashes out at Gabi for lying about Will's child, and Rafe defends his sister. Soon after, Rafe is visciously assaulted and slips into a coma. Kate blames Stefano for the attack, but is shocked to discover that he had no clue when she accidentally tells him about her and Rafe. The culprit was actually Nick's former cellmate, who thought Rafe was Nick. Stefano plotted revenge on Rafe and had Rafe's cop buddy, Joseph Bernardi, who was also on Stefano payroll, use a straight edge razor to cut "it" off. Bernardi was shot by Sami and later died on the operating table. Sami was charged with murder, and when Rafe woke up, he believed Sami was innocent. Jordan Ridgeway, a physical therapist, was hired to get Rafe back on his feet. Rafe eventually fell for Jordan and they started dating.
- Arianna Hernandez (sister, deceased)
- Dario Hernandez (brother)
- Gabi Hernandez (sister)
- Sami Brady (ex-wife, because she cheated on him with EJ)
- Carrie Brady Reed (ex-girlfriend, because she loved Austin and is carrying his baby)
- Nicole DiMera (best friend)
- Daniel Jonas (friend)
- Austin Reed (friend; former enemy)
- EJ DiMera (sworn enemy/rival
- Stefano DiMera (sworn enemy)